Ph.D. Biological Science

University of California San Diego

La Jolla, CA, USA

2015 - 2009

B.S. Biological Science

Xiamen University

Xiamen, Fujian, China

2009 - 2005

Semi-Independent Informatics Fellow

Jay Hesselberth’s Supervision

University of Colorado Anschutz

Current - 2017

• Development of bioinformatics software packages
• RNA post-transcriptional dynamics modeling of steroidogenesis
• RNA-seq analysis and transcriptome annotation improvements for hibernating ground squirrel brain
• Collaboration on various RNA biology projects

Postdoctoral Research Fellow

Judy Lieberman’s Lab

Harvard Medical School

2017 - 2016

• Identification of the mitochondrial trigger of apoptotic mRNA decay
• Purification of cytotoxic granules and key cytolytic proteins
• Mouse genetic manipulation by CRISPR-Cas9, and automated genotyping with custom R app

Graduate Research Assistant

Jens Lykke-Andersen’s Lab

University of California San Diego

2015 - 2009

• Investigation of co-factors involved in ZFP36 (TTP)-mediated mRNA decay and translational repression during the immune response of macrophages
• Characterization of the ZFP36 family proteins in cell cycle progression regulation of mouse embryonic fibroblasts

Undergraduate Research Assistant

Ruichuan Chen’s Lab

Xiamen University

2009 - 2007

• Exploration of cell cycle and apoptosis implications of the transcription elongation regulator HEXIM1
• Mechanistic characterization of p-TEFb activation by HIV-Tat

Online Lecture Instructor (Graduate Level Courses)

University of Colorado Anschutz

N/A

Current - 2020

• Informatics and Statistics for Molecular Biology (2020) - teaching and grading on RStudio Cloud platform
• Foundations in Biomedical Sciences (2020) - Zoom lecture, paper discussion, and exam/homework design on RNA biology
• Workshop for scRNA-seq Data Analysis (2020) - course development and online lectures

Lecture Instructor (Graduate Level Courses)

University of Colorado Anschutz

N/A

Current - 2018

• Rigor in Research (2020) - lecture on RNA sequencing
• Foundations in Biomedical Sciences (2018, 2019) - lectures, paper discussion, and exam/homework design on RNA biology
• Practical Data Analysis with R/RStudio (2018, 2019) - course development and lectures
• Workshop for scRNA-seq Data Analysis (2019) - course development and lectures

Teaching Assistant (Graduate Level Courses)

University of Colorado Anschutz

N/A

Current - 2018

• Practical Computational Biology for Biologists: R (2018, 2019)
• Practical Computational Biology for Biologists: Python (2018, 2019)
• Paper discussion for Core Topics in Biomedical Sciences (2018)

Weekly RNA Bioscience Initiative Informatics Office Hour

University of Colorado Anschutz

N/A

Current - 2017

• Guidance on RNA and computational research questions from students and researchers of CU Anschutz Medical Campus

Teaching Assistant (Undergraduate Level Courses)

University of California San Diego

N/A

2012 - 2011

• Molecular Biology (2012)
• DNA Recombination Lab (2011, 2012)

RNA Bioscience Initiative Internship Mentoring

University of Colorado Anschutz

N/A

Current - 2020

• Mentoring of undergraduate computer science student, systemically exploring published scRNA-seq cell type signatures in the NCBI Gene Expression Omnibus
• Mentee’s work was integrated into updates to R Bioconductor packages clustifyr and clustifyrdatahub
• Mentoring is continuing beyond summer intern period, now focusing on manuscript preparation, poster presentation, and further scRNA-seq software development

Summer Research Mentoring

Harvard Medical School

N/A

2017

• Mentoring of high school student enrolled in the MIT Research Science Institute program in tissue culture, RNA-related bench experiments, RNA-seq informatics analysis, and scientific writing

BS/MS Student Research Mentoring

University of California San Diego

N/A

2015 - 2013

• Mentoring of student research spanning undergraduate honor thesis and master thesis in biochemical investigations of RNA-binding protein functions
• Mentee was awarded Best Poster Presentation Award at 2014 UCSD Biological Sciences Annual Student Research Showcase
• Research project was integrated into the 2016 RNA manuscript, with mentee as second author

RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells

Submitted to Molecular Systems Biology

N/A

2021

• Fu R¹, Wellman K¹, Daigneault J, Hammer G, Rainey B, Riemondy K, Mukherjee N.

Seasonal metabolic reprogramming dominates liver transcriptome dynamics in circannual hibernation

Submitted to Frontiers in Physiology

N/A

2021

• Gillen A¹, Riemondy K¹, Fu R¹, Jeager J, Grabek K, Epperson E, Bustamant C, Hesselberth J, Lazar M, Martin S.

Inclusion of processed cell metadata improves single cell sequencing analysis reproducibility and accessibility

Submitted to biorxiv , Under review at PLOS Biology

N/A

2020

• Puntambekar S, Hesselberth J, Riemondy K^c, Fu R^c.

Dynamic RNA regulation in the brain underlies physiological plasticity in a hibernating mammal

Frontiers in Physiology

N/A

2020

• Fu R¹, Gillen A¹, Grabek K, Riemondy K, Epperson E, Bustamant C, Hesselberth J, Martin S.

clustifyr: an R package for automated single-cell RNA sequencing cluster classification

F1000Research

N/A

2020

• Fu R, Gillen A, Sheridan R, Tian C, Daya M, Hao Y, Hesselberth J, Riemondy K.

PNPT1 release from mitochondria during apoptosis triggers decay of poly(A) RNAs

Cell

N/A

2018

• Liu X¹, Fu R¹, Pan Y, Meza-Sosa K, Zhang Z, Lieberman J.

Recruitment of the 4EHP-GYF2 cap-binding complex to tetraproline motifs of tristetraprolin promotes repression and degradation of mRNAs with AU-rich elements

RNA

N/A

2016

• Fu R, Olsen MT, Webb K, Bennett E, Lykke-Andersen J.

BTK signaling regulates real-time microglial dynamics and prevents demyelination in a novel in vivo model of antibody-mediated cortical demyelination

In prep for Nature Medicine

N/A

2021

• Barr H, Given K, McClain C, Gruber R, Ofengeim D, Fu R, Macklin W, Bennett J, Owens G, Hughes E

Srsf3 mediates alternative RNA splicing downstream of PDGFRa signaling

Submitted to biorxiv and Developmental Cell

N/A

2020

• Dennison B, Larson E, Fu R, Mo J, Fantauzzo K.

Molecular tracking devices quantify antigen distribution and archiving in the lymph node

Submitted to biorxiv, Revision at eLife

N/A

2020

• Walsh S, Sheridan R, Doan T, Lucas E, Ware B, Fu R, Burchill M, Hesselberth J, Tamburini B.

Single-cell RNA sequencing identifies macrophage transcriptional heterogeneities in granulomatous diseases

Revision at American Journal of Respiratory and Critical Care Medicine

N/A

2020

• Liao S, Shaikh A, Konigsberg I, Fu R, Davidson E, Li L, Mould K, Fontenot A, Maier L, Yang I.

Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Acute Myeloid Leukemia Patients

Cancer Discovery

N/A

2019

• Pei S, Pollyea D, Gustafson A, Stevens B, Minhajuddin M, Fu R, Riemondy K, Gillen A, Sheridan R, Kim J, Costello J, Amaya M, Inguva A, Winters A, Ye H, Krug A, Jones C, Adane B, Khan N, Ponder J, Schowinsky J, Abbott D, Hammes A, Myers J, Ashton J, Nemkov T, D’Alessandro A, Gutman J, Fesik S, Ramsey H, Savona M, Smith C, Jordan C.

Chronic Liver Disease in Humans Causes Expansion and Differentiation of Liver Lymphatic Endothelial Cells

Frontiers in Immunology

N/A

2019

• Tamburini B, Finlon JM, Gillen A, Kriss M, Riemondy K, Fu R, Schuyler R, Hesselberth J, Rosen H, Burchill M.

Single cell RNA Sequencing Identifies Transforming Growth Factor β as a Critical Regulator of Alveolar Regeneration

JCI Insight

N/A

2019

• Riemondy K, Jansing N, Jiang P, Redente E, Gillen A, Fu R, Anthony G, Hesselberth J, Zemans R.

Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries.

Nucleic Acid Research

N/A

2019

• Riemondy K, Ransom M, Alderman C, Gillen A, Fu R, Finlay-Schultz J, Kirkpatrick G, Di Paola J, Kabos P, Sartorius C, Hesselberth J.

clustifyr2.0: leveraging GEO deposited single cell data for automated cell type classification

Keystone eSymposia on Single Cell Biology (Poster)

N/A

2021

Towards a comprehensive view of dynamic RNA regulation in hibernating 13-lined ground squirrel

EMBL Conference, From Functional Genomics to Systems Biology (Poster)

N/A

2020

ClustifyR: automated single-cell RNA sequencing cluster classification

Keystone Symposia on Single Cell Biology (Poster)

N/A

2019

PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA and poly(A)-tailed ncRNA during apoptosis

Boston Children’s Hospital PCMM Research Poster Session (Poster)

N/A

2017

PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA during apoptosis

Boston Children’s Hospital PCMM Research Poster Session (Poster)

N/A

2016

TTP-mediated mRNA repression involves recruitment of the 4EHP-GYF2 complex

Cold Spring Harbor Laboratory mRNA Processing Meeting (Presentation)

N/A

2015

TTP represses translation of target mRNAs through the 4EHP-GYF2 complex

UCSD Mechanisms of Gene Expression Seminar (Presentation)

N/A

2014

TTP family proteins regulate the stability of retinoblastoma protein mRNAs during serum-stimulated G₀-S transition

Cold Spring Harbor Laboratory mRNA Processing Meeting (Poster)

N/A

2013

The regulation of TTP family mRNA-decay factors during G₀-S cell cycle progression

Keystone Symposia on Protein-RNA Interactions (Poster)

N/A

2012

Organizer for CU Anschutz Immuno-Informatics Joint Journal Club

N/A

N/A

Current - 2020

RNA Bioscience Initiative Grant Review

N/A

N/A

Current - 2019

GENETICS Early Career Reviewer (Cellular Genetics section)

4 manuscripts reviewed for GENETICS and G3, tinyurl.com/rev-rf

N/A

Current - 2018

Peer review of manuscripts under Dr Lykke-Andersen, Dr Lieberman, Dr Hesselberth

N/A

N/A

Current - 2011

Organizer for UCSD Ethics Center’s Silent Spring (50th Anniversary) Project

N/A

N/A

2012

RNA Society Volunteer - Writer for Scientist Spotlight

N/A

N/A

Current - 2020

CU Anschutz Medical Campus Equity Certificate Program training

N/A

N/A

2021

Admissions Committee for CU Graduate Experiences for Multicultural Students

N/A

N/A

2019

Mentor for CU Anschutz and Denver Campus ISCORE (undergraduate mentorship program)

N/A

N/A

2019

BioFrontiers Hackathon

N/A

N/A

2018

Data Incubator Data Science Fellowship

N/A

N/A

2017

Grant writing training under Dr Lieberman

N/A

N/A

2016

Harvard Medical School Scientists Teaching Science Course

N/A

N/A

2016

Dr Huang Memorial Scholarship, UC San Diego

N/A

N/A

2011 - 2009

National College Students Creativity Experiment Project

N/A

N/A

2009 - 2007

First-Class Scholarship

N/A

N/A

2008 - 2006

XMU University Merit Student

N/A

N/A

2008 - 2006

Volunteer for CU Anschutz Medical Campus Young Hands in Science Outreach Program

N/A

N/A

Current - 2021

Facilitator at Denver Museum of Nature and Science - Prehistoric Journey section

N/A

N/A

2020 - 2019

Visitor Education Volunteer at the New England Aquarium

N/A

N/A

2017 - 2016

Information Ambassador at the San Diego Zoo

N/A

N/A

2016 - 2015